1. A Short Introduction to Analyzing Biological Data Using Relational Databases
Part III: Writing Simple (Single Table) Queries to Access Relational Data
Alex Ropelewski
Pittsburgh Supercomputing Center
National Resource for Biomedical Supercomputing
Bienvenido Vélez
University of Puerto Rico at Mayaguez
Department of Electrical and Computer Engineering

3. Learning Objectives Using SQL SELECT statement to:
Select which attributes to show in a result
Select which rows to show in a result
Using UPDATE to modify rows
Using DELETE to remove rows
Using logical operators (AND, OR and NOT) to form more complex selections of rows
Using INTO clause to store result rows into new database tables

4. The language of relational databases
SQL
The language of relational databases
Data definition/schema creation
Implements relational algebra operations
Data manipulation
Insertion
Manipulation
Updates
Removals
A standard (ISO) since 1987

5. An Improved Relational Database Design
Sequences
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Human
P81479
Phospholipase A2 isozyme IV
Indian Green Tree Viper
P00623
Phospholipase A2
Eastern Diamondback Rattlesnake
Matches
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 E-52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Runs
RunNum
Date
Matrix 1
7/21/07
Pam70 2
7/20/07
Blosom80

6. SQL: SELECT Statement Selects attributes
SELECT Accession, Description, Species FROM Sequences
In this context since we are selecting all attributes in the table. We could use the wildcard character * instead of listing the individual attribute names:
SELECT * FROM Sequences
Sequences
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Human
P81479
Phospholipase A2 isozyme IV
Indian Green Tree Viper
P00623
Phospholipase A2
Eastern Diamondback Rattlesnake

7. Used to filter tuples with certain attribute values
SQL: WHERE Clause
Used to filter tuples with certain attribute values
Used in many SQL Statements, including SELECT
SELECT * FROM Sequences WHERE Species=’Human’
Sequences
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Human

8. Used to order data by attribute values
SQL: ORDER BY Clause
Used to order data by attribute values
Used in many SQL Statements, including SELECT
SELECT * FROM Sequences ORDER BY Species
Sequences
Accession
Description
Species
P00623
Phospholipase A2
Eastern Diamondback Rattlesnake
P14555
Group IIA Phospholipase A2
Human
P81479
Phospholipase A2 isozyme IV
Indian Green Tree Viper

9. SQL: UPDATE Statement Revises table data
Sequences (before UPDATE)
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Human
UPDATE Sequences SET Species=’Homo Sapiens’
WHERE Accession=’P14555’
Sequences (after UPDATE)
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Homo Sapiens

10. Removes table data – Be Careful!
SQL: DELETE Statement
Removes table data – Be Careful!
Sequences (before DELETE)
Accession
Description
Species
P14555
Group IIA Phospholipase A2
Human
P81479
Phospholipase A2 isozyme IV
Indian Green Tree Viper
P00623
Phospholipase A2
Eastern Diamondback Rattlesnake
DELETE FROM Sequences WHERE Accession=’P14555’
Sequences (after DELETE)
Accession
Description
Species
P81479
Phospholipase A2 isozyme IV
Indian Green Tree Viper
P00623
Phospholipase A2
Eastern Diamondback Rattlesnake

11. Used in many SQL Statements One of two conditions must be met
SQL: OR operator
Used in many SQL Statements
One of two conditions must be met
SELECT * FROM Matches
WHERE Accession=’P14555’ OR Accession=’P00623’
Matches
Select Result
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 -E52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Accession
RunNum
eValue
P14555 1
4.18 E-32 2
3.47 E-33
P00623
1.21 E-08

12. Used in many SQL Statement Two of two conditions must be met
SQL: AND operator
Used in many SQL Statement
Two of two conditions must be met
SELECT * FROM Matches
WHERE Accession=’P14555’ AND RunNum=’1’
Matches
Select Result
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 -E52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Accession
RunNum
eValue
P14555 1
4.18 E-32

13. Used in many SQL Statement Negation of condition
SQL: NOT operator
Used in many SQL Statement
Negation of condition
SELECT * FROM Matches
WHERE NOT Accession=’P14555’
Matches
Select Result
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 -E52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Accession
RunNum
eValue
P81479 2
2.68 -E52 1
1.20 E-54
P00623
1.21 E-08

14. Used to clarify order of operations
SQL: Parenthesis
Used to clarify order of operations
SELECT * FROM Matches
WHERE ((Accession=’P14555’) OR (Accession=’P81479’))
AND RunNum=’2’
Matches
Select Result
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 -E52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Accession
RunNum
eValue
P14555 2
3.47 E-33
P81479
2.68 E-52

15. Used to store results in new tables
SQL: INTO
Used to store results in new tables
SELECT * INTO GoodMatches
FROM Matches
WHERE (eValue >= 1.0E-10)
Matches
GoodMatches Table
Accession
RunNum
eValue
P14555 1
4.18 E-32
P81479 2
2.68 -E52
3.47 E-33
1.20 E-54
P00623
1.21 E-08
Accession
RunNum
eValue
P00623 2
1.21 E-08

16. Key Concepts
SQL’s SELECT statement can be used to select which attibutes should appear in a result
SQL’s SELECT statement can be used to select which rows should appear in a result using the WHERE clause
SQL’s UPDATE statement can be used to modify rows
SQL’s DELETE statement can be used to remove rows
Logical operators can be used to form complex logical conditions for selecting which rows to show in a result
The INTO clause can be used to store results into a new table in the database